3M1V
Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005737 | cellular_component | cytoplasm |
A | 0015948 | biological_process | methanogenesis |
A | 0016740 | molecular_function | transferase activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0015948 | biological_process | methanogenesis |
B | 0016740 | molecular_function | transferase activity |
B | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0015948 | biological_process | methanogenesis |
C | 0016740 | molecular_function | transferase activity |
C | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0015948 | biological_process | methanogenesis |
D | 0016740 | molecular_function | transferase activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
E | 0005737 | cellular_component | cytoplasm |
E | 0015948 | biological_process | methanogenesis |
E | 0016740 | molecular_function | transferase activity |
E | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
F | 0005737 | cellular_component | cytoplasm |
F | 0015948 | biological_process | methanogenesis |
F | 0016740 | molecular_function | transferase activity |
F | 0050524 | molecular_function | coenzyme-B sulfoethylthiotransferase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 551 |
Chain | Residue |
A | HOH1356 |
A | HOH1590 |
A | HOH1599 |
A | HOH2583 |
A | HOH2603 |
A | HOH3581 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE MG A 552 |
Chain | Residue |
A | HOH2285 |
A | HOH3581 |
A | HOH3828 |
A | HOH3971 |
A | ACT555 |
A | HOH718 |
A | HOH1599 |
site_id | AC3 |
Number of Residues | 39 |
Details | BINDING SITE FOR RESIDUE F43 A 1 |
Chain | Residue |
A | ALA144 |
A | VAL145 |
A | VAL146 |
A | GLN147 |
A | GLN230 |
A | MET233 |
A | ALA243 |
A | HOH582 |
A | HOH650 |
A | HOH673 |
A | HOH675 |
A | HOH697 |
A | HOH702 |
A | HOH788 |
D | GLY326 |
D | GLY327 |
D | VAL328 |
D | GLY329 |
D | PHE330 |
D | THR331 |
D | GLN332 |
D | TYR333 |
D | PHE396 |
D | GLY397 |
D | GLY442 |
D | PHE443 |
D | COM554 |
D | HOH664 |
E | SER365 |
E | ILE366 |
E | TYR367 |
F | LEU117 |
F | SER118 |
F | GLY119 |
F | LYS153 |
F | SER154 |
F | VAL155 |
F | HIS156 |
F | HIS158 |
site_id | AC4 |
Number of Residues | 35 |
Details | BINDING SITE FOR RESIDUE TP7 A 553 |
Chain | Residue |
A | ARG270 |
A | LEU320 |
A | MET324 |
A | SER325 |
A | PHE330 |
A | PHE443 |
A | MET480 |
A | ASN481 |
A | VAL482 |
A | HOH588 |
A | HOH603 |
A | HOH619 |
A | HOH654 |
A | HOH682 |
A | HOH3683 |
A | HOH3684 |
A | HOH4087 |
A | HOH4092 |
A | HOH4093 |
A | HOH4094 |
A | HOH4095 |
A | HOH4096 |
B | PHE362 |
B | TYR367 |
B | GLY368 |
B | GLY369 |
B | HIS379 |
B | ILE380 |
B | HOH4089 |
B | HOH4091 |
D | ARG225 |
D | LYS256 |
D | MHS257 |
D | HOH4088 |
D | HOH4090 |
site_id | AC5 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE COM A 554 |
Chain | Residue |
A | TYR333 |
A | PHE443 |
A | TYR444 |
A | HOH3682 |
B | PHE361 |
B | SER365 |
B | TYR367 |
C | LEU117 |
C | ARG120 |
D | F43552 |
site_id | AC6 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE ACT A 555 |
Chain | Residue |
A | PHE537 |
A | GLU538 |
A | MG552 |
A | HOH640 |
A | HOH1396 |
A | HOH2285 |
A | HOH3828 |
A | HOH3971 |
A | HOH3988 |
A | VAL519 |
A | LYS531 |
site_id | AC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE ACT A 556 |
Chain | Residue |
A | LYS256 |
A | HOH4098 |
A | HOH4099 |
A | HOH4100 |
A | HOH4101 |
E | GLY368 |
E | GLY369 |
site_id | AC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE PEG A 557 |
Chain | Residue |
A | TYR348 |
site_id | AC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE ZN A 558 |
Chain | Residue |
A | ARG102 |
A | SER215 |
A | ARG216 |
A | CYS218 |
D | ARG102 |
D | SER215 |
D | ARG216 |
D | CYS218 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG B 444 |
Chain | Residue |
B | HOH1305 |
B | HOH3547 |
B | HOH3548 |
B | HOH3549 |
B | HOH3550 |
B | HOH3714 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG B 445 |
Chain | Residue |
B | ASP271 |
B | HOH564 |
B | HOH811 |
B | HOH1206 |
B | HOH3076 |
B | HOH4178 |
site_id | BC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE ACT B 446 |
Chain | Residue |
B | PHE362 |
B | GLY368 |
B | HOH4089 |
B | HOH4091 |
D | LYS256 |
D | HOH4090 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG C 250 |
Chain | Residue |
C | GLU30 |
C | HOH1095 |
C | HOH3555 |
C | HOH3556 |
C | HOH3557 |
C | HOH3558 |
site_id | BC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ACT C 1 |
Chain | Residue |
A | THR62 |
C | LYS153 |
C | HOH1067 |
C | HOH4052 |
site_id | BC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PEG C 251 |
Chain | Residue |
C | ARG43 |
C | GLU47 |
C | GLU48 |
C | HOH3630 |
C | HOH4323 |
site_id | BC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG D 1 |
Chain | Residue |
D | HOH3543 |
D | HOH3546 |
F | HOH3542 |
F | HOH3545 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG D 551 |
Chain | Residue |
D | HOH1116 |
D | HOH3559 |
D | HOH3560 |
D | HOH3561 |
D | HOH3562 |
D | HOH3563 |
site_id | BC9 |
Number of Residues | 39 |
Details | BINDING SITE FOR RESIDUE F43 D 552 |
Chain | Residue |
A | GLY326 |
A | GLY327 |
A | VAL328 |
A | GLY329 |
A | PHE330 |
A | THR331 |
A | GLN332 |
A | TYR333 |
A | PHE396 |
A | GLY397 |
A | GLY442 |
A | PHE443 |
A | COM554 |
A | HOH597 |
B | SER365 |
B | ILE366 |
B | TYR367 |
C | LEU117 |
C | SER118 |
C | GLY119 |
C | LYS153 |
C | SER154 |
C | VAL155 |
C | HIS156 |
C | HIS158 |
C | HOH647 |
D | ALA144 |
D | VAL145 |
D | VAL146 |
D | GLN147 |
D | GLN230 |
D | MET233 |
D | ALA243 |
D | HOH566 |
D | HOH643 |
D | HOH668 |
D | HOH706 |
D | HOH716 |
D | HOH718 |
site_id | CC1 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE TP7 D 553 |
Chain | Residue |
A | ARG225 |
A | LYS256 |
A | MHS257 |
A | HOH4098 |
A | HOH4099 |
A | HOH4100 |
A | HOH4101 |
D | ARG270 |
D | LEU320 |
D | MET324 |
D | SER325 |
D | PHE330 |
D | PHE443 |
D | MET480 |
D | ASN481 |
D | VAL482 |
D | HOH570 |
D | HOH579 |
D | HOH628 |
D | HOH1070 |
D | HOH3681 |
D | HOH3840 |
D | HOH4097 |
D | HOH4102 |
D | HOH4103 |
D | HOH4104 |
D | HOH4105 |
E | PHE362 |
E | TYR367 |
E | GLY368 |
E | GLY369 |
E | HIS379 |
E | ILE380 |
E | HOH450 |
site_id | CC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE COM D 554 |
Chain | Residue |
A | F431 |
D | TYR333 |
D | PHE443 |
D | TYR444 |
D | HOH760 |
E | PHE361 |
E | SER365 |
E | TYR367 |
F | LEU117 |
F | ARG120 |
site_id | CC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE EDO D 555 |
Chain | Residue |
D | TYR348 |
site_id | CC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG E 444 |
Chain | Residue |
E | HOH2200 |
E | HOH2328 |
E | HOH3583 |
E | HOH3584 |
E | HOH3585 |
site_id | CC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG F 250 |
Chain | Residue |
F | GLU30 |
F | HOH1294 |
F | HOH3551 |
F | HOH3552 |
F | HOH3553 |
F | HOH3554 |
site_id | CC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE EDO F 251 |
Chain | Residue |
F | ARG43 |
F | GLU47 |
F | GLU48 |
site_id | CC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE EDO F 252 |
Chain | Residue |
F | LYS132 |
F | HOH1243 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y |
Chain | Residue | Details |
C | ARG120 | |
F | ARG120 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27140643, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y, ECO:0007744|PDB:5G0R |
Chain | Residue | Details |
B | GLY369 | |
E | GLY369 | |
D | ARG225 | |
D | LYS256 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: in chain B => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27140643, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y, ECO:0007744|PDB:5G0R |
Chain | Residue | Details |
A | ARG270 | |
D | ARG270 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y |
Chain | Residue | Details |
A | TYR333 | |
A | TYR444 | |
D | TYR333 | |
D | TYR444 |
site_id | SWS_FT_FI5 |
Number of Residues | 2 |
Details | MOD_RES: Pros-methylhistidine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
Chain | Residue | Details |
A | MHS257 | |
D | MHS257 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | MOD_RES: 5-methylarginine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
Chain | Residue | Details |
A | AGM271 | |
D | AGM271 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: 2-methylglutamine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
Chain | Residue | Details |
A | MGN400 | |
D | MGN400 |
site_id | SWS_FT_FI8 |
Number of Residues | 2 |
Details | MOD_RES: 1-thioglycine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
Chain | Residue | Details |
A | GL3445 | |
D | GL3445 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: (Z)-2,3-didehydroaspartate => ECO:0000269|PubMed:27467699 |
Chain | Residue | Details |
A | ASP450 | |
D | ASP450 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: S-methylcysteine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
Chain | Residue | Details |
A | SMC452 | |
D | SMC452 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 1 |
Details | M-CSA 156 |
Chain | Residue | Details |
B | TYR367 | electrostatic stabiliser, proton acceptor, proton donor, proton relay, radical stabiliser |
A | TYR333 | electrostatic stabiliser, radical stabiliser |
A | GL3445 | single electron acceptor, single electron donor, single electron relay |
A | ASN481 | activator, electrostatic stabiliser, proton acceptor, proton donor, proton relay |
site_id | MCSA2 |
Number of Residues | 1 |
Details | M-CSA 156 |
Chain | Residue | Details |
E | TYR367 | electrostatic stabiliser, proton acceptor, proton donor, proton relay, radical stabiliser |
D | TYR333 | electrostatic stabiliser, radical stabiliser |
D | GL3445 | single electron acceptor, single electron donor, single electron relay |
D | ASN481 | activator, electrostatic stabiliser, proton acceptor, proton donor, proton relay |